Development of Fast-JX in GEOS-Chem: Difference between revisions

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(New page: This page describes the implementation of Fast-JX in GEOS-Chem. ==A few things about Fast-JX== I implemented Fast-JX (v6.2) into GEOS-Chem v8-01-02. This version of Fast-JX includes 18 bi...)
 
 
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This page describes the implementation of Fast-JX in GEOS-Chem.
On this page we provide links to pages describing the implementation of FAST-JX in GEOS-Chem.


==A few things about Fast-JX==
== Implementation of FAST-JX v7.0 ==
I implemented Fast-JX (v6.2) into GEOS-Chem v8-01-02. This version of Fast-JX includes 18 bins of wavelengths. A few reasons:
* This version can be used for stratospheric chemistry with 11 wavelength bins in UV.
* This version of Fast-JX handles thick clouds much better, because it uses a log-spacing to add sub-layers for thick clouds or aerosol layers.
* This version of Fast-JX is supposed to do a better job over polar region.
* I combined most files into one module: fast_jx_mod.f. This will provide a much better platform to get updates from newer version of Fast-JX.
* Fast-JX takes into account the photolysis of O2, which will make a little bit more ozone in upper troposphere.
If you need the source code, please contact [mailto:Jingqiu.Mao@noaa.gov Jingqiu Mao] on this.


==How does the new Fast-JX work?==
This discussion has been moved to our [[FAST-JX v7.0 photolysis mechanism]] wiki page.
Fast-JX calculates scattering at '''five wavelength 200nm, 300nm, 400nm, 600nm and 999nm'''. Fast-J calculates at four wavelength 300nm, 400nm, 600nm and 999nm (without 200nm).
# In chemdr.f, Fast-JX is initialized (call INPHOT(LLTROP, NPHOT)).
# In chemdr.f, Fast-JX is calculated by calling FAST_J( SUNCOS, OPTD, UVALBEDO).
# In fast_j.f, it was first determined which cloud overlap scheme (linear, random,or maximum) to be used. Then send single column properties to PHOTOJ for calculation, including:
## pressure profile
## temperature profile
## surface albedo
## Aerosol OD profile
## Mineral dust OD profile
## Cloud OD profile
# In calcrate.f, send J-values to smvgear by calling fjfunc.f.


===Modules in fast_jx_mod.f===
--[[User:Bmy|Bob Y.]] 11:15, 20 May 2014 (EDT)
* INPHOT
** Read in labels of photolysis (call RD_JS)
** Match Fast-JX species with Harvard species (call JV_INDEX)
** Read in Fast-JX X-sections (spectral data) (call RD_XXX)
** Read in T & O3 climatology (call RD_PROF)
** Select aerosol/cloud types to be used (call SET_AER)
 
* PHOTOJ
** Set up Air, O3, BC profiles on GEOS-Chem vertical levels (call set_prof.f), this is the same as the old fast-j.
** calculate air mass factors by calling sphere2. This is different from the old fast-j: the new AMF2 does each of the half-layers of the CTM separately, whereas the original, based on the pratmo code did the whole layers and thus calculated the ray-path to the CTM layer edges, NOT the middle.
** add sub-layers (JXTRA) to thick cloud/aerosol layers by calling  EXTRAL. This version sets up log-spaced sub-layers of increasing thickness ATAU. Given the aerosol+cloud OD/layer in visible (600 nm) calculate how to add additonal levels at top of clouds (now uses log spacing). This was linear spacing in Fast-J, so caused lots of problems for thick clouds.
** For each wavelength bin, call OPMIE to calculate the mean actinic flux in each layer (AVGF), then save the flux into FFF (1:LPAR).
** call JRATET to convert FFF to J-values for all species.
 
==How does the current Fast-J work in GEOS-Chem?==
 
===Step 1: inphot.f ===
''Require input files ('''cmn_fj.h, jv_cmn.h, ratj.d, jv_spec.dat, jv_atms.dat''')''
# Error check # of layers (call ERROR_STOP)
# Read in labels of photolysis rates required (call RD_JS.f)
# translate between GEOS-Chem species nomenclature and Fast-J species nomenclature(call JV_INDEX.f)
# Read in JPL spectral data set (e.g. X-sections, quantum yields) (call RD_TJPL.f)
# Read in T & O3 climatology (cf. Nagatani/92 and McPeters/91) (call RD_PROF.f)
# Select Aerosol/Cloud types to be used (call SET_AER.f)
 
===Step 2: fast_j.f===
For each (NLON,NLAT) location, call subroutine PHOTOJ (in a parallel loop to compute J-values for the entire column. J-values will be stored in the common-block variable ZPJ, and will be later accessed via function FJFUNC).
# Read TOMS O3 columns if it's a new month(call READ_TOMSO3 from "toms_mod.f“).
# Cloud overlap options
::* Linear Approximation (used up to v7-04-12)->call photoj.f
::* Approximate Random Overlap (default)->call photoj.f
::* Maximum Random Overlap (MRAN, computation intensive)->call photoj.f+mmran_16.f
 
===Step 3: photoj.f===
* Set up Air, O3, BC profiles on GEOS-Chem vertical levels (call set_prof.f)
::* Set up cloud and surface properties (Call CLDSRF.f).
::* Set up pressure levels for O3/T climatology.
::* Select appropriate monthly and latitudinal profiles
::* Apportion O3 and T on supplied climatology z* levels onto CTM levels with mass (pressure) weighting, assuming constant mixing ratio and temperature half a layer on either side of the point supplied.
::* Calculate effective altitudes using scale height at each level
::* Add aerosol column - include aerosol types here. Currently use soot water and ice; assume black carbon x-section of 10 m2/g, independent of wavelength; assume limiting temperature for ice of -40 deg C.
::* Calculate column quantities for FAST-J: monthly mean air column and monthly mean O3 column.
::* Weight the O3 column by the observed monthly mean TOMS data.
::* Interpolate O3 column to current day (TOMS data is half month time resolution). Scale monthly O3 profile to the daily O3 profile.
 
* Compute actinic flux at each GEOS-CHEM vertical level (call JVALUE.f). In which, calculate air mass factors for each layer (call sphere.f). Loop over all wavelength bins to call OPMIE.f:
::* Pick nearest Mie wavelength, no interpolation.
::* For Mie code scale extinction at 1000 nm to wavelength WAVEL (QXMIE)
::* Set up total optical depth over each CTM level, DTAUX
::* Fractional extinction for Rayleigh scattering and each aerosol type
::* Define the scattering phase fn. with mix of Rayleigh(1) & Mie(MIEDX), No. of quadrature pts fixed at 4 (M__), expansion of phase fn @ 8
::* Calculate attenuated incident beam EXP(-TTAU/U0) and flux on surface
::* Take optical properties on CTM layers and convert to a photolysis level grid corresponding to layer centres and boundaries
::* Calculate cumulative total and define levels we want J-values at. Sum upwards for levels, and then downwards for Mie code readjustments.
::* SET UP FOR MIE CODE. Transpose the ascending TTAU grid to a descending ZTAU grid. This is required so that J-values can be calculated for the centre of CTM layers; the index of these layers is kept in the jndlev array.
::* Insert new levels, working downwards from the top of the atmosphere to the surface (down in 'j', up in 'k').
::* call MIESCT.f
:::(1) fix scattering to 4 Gauss pts = 8-stream(CALL GAUSSP.f)
:::(2) solve eqn of R.T. only for first-order M=1(call LEGND0.f)
:::(3) call BLKSLV.f to solve the block tri-diagonal system.
:::(4) call GEN.f and MATIN4.f.
 
* Calculate J-values for all species(call JRATET.f)
::* Scale actinic flux (FFF) by Solar distance factor (SOLF)
::* With model temperature, call XSECO2.f(FLINT.f); call XSECO3.f(FLINT.f); call XSEC1D.f(FLINT.f)
::* Calculate Jvalues for O2,O3,O1D
::* Calculate remaining J-values with T-dep X-sections
 
=== Step 4: fjfunc.f===
supplies J-values to SMVGEAR solver
 
==Implementation of Fast-JX==
===New input files===
# spec2008.dat: fast-J X-sections (spectral data)
# atmos_std.dat: T & O3 climatology data
# chemJ2008.d: this is a tranfer map from the J's automatically calculated in fast-JX onto the names and order in the users chemistry code.
 
===Major changes===
* '''Aerosol_mod.f'''
{| border="1" cellspacing="0" cellpadding="5"
|-bgcolor="#cccccc"
!width="450pt"|'''old'''
!width="450pt"|'''new'''
|-
|<nowiki># include "cmn_fj.h" # include "jv_cmn.h" </nowiki>||<nowiki>#    include "fj2008.h"</nowiki>
|-
|RW(R) = RAA('''4''',IND(N)+R-1)||RW(R) = RAA('''5''',IND(N)+R-1)
|-
|QW(R) = QAA('''4''',IND(N)+R-1)*FWET + QAA('''4''',IND(N))*(1.d0-FWET)||QW(R) = QAA('''5''',IND(N)+R-1)*FWET + QAA('''5''',IND(N))*(1.d0-FWET)
|-
|WAERSL(I,J,L,N) * QAA('''4''',IND(N))||WAERSL(I,J,L,N) * QAA('''5''',IND(N))
|-
|DAERSL(I,J,L,N-1) * QAA('''4''',IND(N))||DAERSL(I,J,L,N-1) * QAA('''5''',IND(N))
|-
|REFF = 1.0D-4 * RAA('''4''',IND(N))||REFF = 1.0D-4 * RAA('''5''',IND(N))
|-
|QAA('''2''',IND(N)+R-1) / QAA('''4''',IND(N)+R-1)||QAA('''3''',IND(N)+R-1) / QAA('''5''',IND(N)+R-1)
|}
 
All these are because there is one more wavelength bin for mie scattering(200nm), so RAA (effective radius) and QAA(aerosol extinction coefficient) all need to be changed accordingly.
* '''dust_mod.f'''
{| border="1" cellspacing="0" cellpadding="5"
|-bgcolor="#cccccc"
!width="450pt"|'''old'''
!width="450pt"|'''new'''
|-
|<nowiki># include "cmn_fj.h" # include "jv_cmn.h" </nowiki>||<nowiki>#    include "fj2008.h"</nowiki>
|-
|DUST(I,J,L,N) * QAA('''4''',14+N)/ ( MSDENS(N) * RAA('''4''',14+N) * 1.0D-6 ) || DUST(I,J,L,N) * QAA('''5''',14+N)/ ( MSDENS(N) * RAA('''5''',14+N) * 1.0D-6 )
|-
|ERADIUS(JLOOP,N) = RAA('''4''',14+N) * 1.0D-4||ERADIUS(JLOOP,N) = RAA('''5''',14+N) * 1.0D-4
|-
|( ODMDUST(I,J,L,N) * QAA('''2''',14+N) / QAA('''4''',14+N) )||( ODMDUST(I,J,L,N) * QAA('''3''',14+N) / QAA('''5''',14+N) )
|-
|DUST(I,J,L,N) * QAA('''4''',14+N) / ( MSDENS(N) * RAA('''4''',14+N) * 1.0D-6 )||DUST(I,J,L,N) * QAA('''5''',14+N)/ ( MSDENS(N) * RAA('''5''',14+N) * 1.0D-6 )
|-
|ERADIUS(JLOOP,N) = RAA('''4''',14+N) * 1.0D-4||ERADIUS(JLOOP,N) = RAA('''5''',14+N) * 1.0D-4
|-
|( ODMDUST(I,J,L,N) * QAA(2,14+N) / QAA(4,14+N) )||( ODMDUST(I,J,L,N) * QAA(3,14+N) / QAA(5,14+N) )
|}
 
* '''fast_j.f, fjfunc.f, fjfunc.f'''
{| border="1" cellspacing="0" cellpadding="5"
|-
| ||USE FAST_JX_MOD,  ONLY : PHOTOJ
|-
|<nowiki># include "cmn_fj.h" # include "jv_cmn.h" </nowiki>||<nowiki># include "fj2008.h"</nowiki>
|}
 
 
* '''fast_jx_mod.f- this is a new file and it is the main file for Fast-J.'''
 
 
* '''planeflight_mod.f'''
{| border="1" cellspacing="0" cellpadding="5"
|-bgcolor="#cccccc"
!width="450pt"|'''old'''
!width="450pt"|'''new'''
|-
|<nowiki># include "cmn_fj.h" # include "jv_cmn.h" </nowiki>||<nowiki># include "fj2008.h"</nowiki>
|-
|S400nm  = QAA('''2''',IND(N)+RH-1) / &  QAA('''4''',IND(N)+RH-1)||S400nm  = QAA('''3''',IND(N)+RH-1) / &  QAA('''5''',IND(N)+RH-1)
|-
|S400nm  = QAA('''2''',IND(N)+RH-1) / &  QAA('''4''',IND(N)+RH-1)||S400nm  = QAA('''3''',IND(N)+RH-1) / &  QAA('''5''',IND(N)+RH-1)
|}
 
===Other related changes===
* '''ch3i_mod.f'''
add this line at the beginning;
“USE FAST_JX_MOD”
Because ch3i_mod.f needs fast_j to calculate something for ch3i simulations.
* '''Chemdr.f'''
Add this line:  
“USE FAST_JX_MOD,          ONLY : INPHOT”
Because inphot.f is now merged into fast_jx_mod.f
* '''chemistry_mod.f'''
Add this line:
USE FAST_JX_MOD
* '''diag48_mod.f, diag49_mod.f, diag50_mod.f, diag51_mod.f'''
{| border="1" cellspacing="0" cellpadding="5"
|-bgcolor="#cccccc"
!width="450pt"|'''old'''
!width="450pt"|'''new'''
|-
| ||USE FAST_JX_MOD,  ONLY : PHOTOJ
|-
|<nowiki># include "cmn_fj.h" # include "jv_cmn.h" </nowiki>||<nowiki># include "fj2008.h"</nowiki>
|}
 
===Files removed from v8-01-02===
{| border="1" cellspacing="0" cellpadding="5"
|-bgcolor="#cccccc"
!width="250pt"|'''Filename'''
!width="500pt"|'''Notes'''
|-
|BLKSLV.f||Merged into “fastjx_mod.f”
|-
|CLDSRF.f||Merged into “fastjx_mod.f”
|-
|cmn_fj.h||Input files, now merged into “fj2008.h”.
|-
|EFOLD.f||Removed, not even used in fast-j
|-
|FLINT.f||Merged into “fastjx_mod.f” (Three-point linear interpolation function)
|-
|GAUSSP.f||Merged into “fastjx_mod.f”
|-
|GEN.f ||Merged into “fastjx_mod.f”
|-
|inphot.f||Merged into “fastjx_mod.f”
|-
|JRATET.f||Merged into “fastjx_mod.f”
|-
|JVALUE.f||Merged into PHOTOJ in “fastjx_mod.f”
|-
|jv_cmn.h||Input files, now merged into “fj2008.h”.
|-
|jv_index.f||Merged into “fastjx_mod.f”
|-
|jv_mie.h||Input files, now merged into “fj2008.h”.
|-
|LEGND0.f||Merged into “fastjx_mod.f”
|-
|MATIN4.f||Merged into “fastjx_mod.f”
|-
|MIESCT.f||Merged into “fastjx_mod.f”
|-
|NOABS.f||Removed, not even used in fast-j
|-
|OPMIE.f||Merged into “fastjx_mod.f”
|-
|photoj.f||Merged into “fastjx_mod.f”
|-
|rd_js.f||Merged into “fastjx_mod.f”
|-
|rd_prof.f||Merged into “fastjx_mod.f”
|-
|RD_TJPL.f||This is changed to “RD_XXX” in “fastjx_mod.f”.
|-
|set_aer.f||Merged into “fastjx_mod.f”
|-
|set_prof.f||Merged into “fastjx_mod.f”
|-
|SPHERE.f||Merged into “fastjx_mod.f”, now changed to sphere2 function.
|-
|XSEC1D.f||Merged into PHOTOJ in “fastjx_mod.f”
|-
|XSECO2.f||Merged into PHOTOJ in “fastjx_mod.f”
|-
|XSECO3.f||Merged into PHOTOJ in “fastjx_mod.f”
|}

Latest revision as of 16:42, 24 June 2024

On this page we provide links to pages describing the implementation of FAST-JX in GEOS-Chem.

Implementation of FAST-JX v7.0

This discussion has been moved to our FAST-JX v7.0 photolysis mechanism wiki page.

--Bob Y. 11:15, 20 May 2014 (EDT)

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